During malignant progression, the pattern of expressed genes can provide clues to understanding tumor growth. In addition to insight into the tumor biology that might be derived from this pattern, there is a practical application for identifying genes highly expressed in tumors but not in normal adult tissue. A common example of tumor marker use is the serum protein assay for early detection of cancer (Kardamakis 1996). Investigators are also searching for genomic DNA alterations or abnormal gene expression in other clinically accessible samples. Progress has been made on finding tumor markers in stool (Sidransky et al. 1992; Vogelstein and Kinzler 1999), sputum (Mao et al. 1994), and urine (Lokeshwar et al. 1997).
Tumor-specific gene expression may also provide an opportunity for immune-based cancer therapies by targeting one or more of the tumor antigens coded for by these genes. Toxic antibodies with high affinity to accessible cell-surface or extracellular proteins may kill enough cancer cells to be therapeutic (Panchal 1998). Recent success with monoclonal antibody targeting of the Her/neu-2 receptor (Herceptin) indicates that targeting a tumor antigen can be useful (Hanna et al. 1999). The approach ideally requires identifying a cell surface protein uniquely expressed on the cells of the tumor, but not expressed in the patient's normal tissue exposed to the antibody during therapy. Also promising is a ‘tumor vaccine’ approach where the goal is to direct immune defenses toward the tumor by educating host antigen presenting cells with tumor-derived material (Gilboa et al. 1998). Expression of the marker on the cell surface is not a requirement of this system, but successful systemic administration of a tumor vaccine might require a relative lack of marker expression in all normal tissue cells, especially within vital organs. Either of these therapeutic approaches could benefit from the discovery of new tumor specific markers.
Tumor markers and antigens have promising clinical utility, but previous techniques for locating these proteins has not yielded robust markers for most cancers (Wu 1999). Finding a candidate marker is frequently the by-product of other studies, but not the initial intent of the research. Furthermore, generating the expression profile for each suspect gene has often relied on time consuming techniques, such as Northern blotting, in situ hybridization, or immunohistochemistry. Fortunately, new genome-scale technology should accelerate tumor marker discovery. In particular, the ability to assay comprehensive gene expression has made significant advances (Gress et al. 1992; Schena et al. 1995; Velculescu et al. 1995; Lockhart et al. 1996; Kononen et al. 1998).
Large-scale gene expression assays, such as cDNA microarrays (Schena et al. 1995), oligonucleotide chips (Lockhart et al. 1996), cDNA library sequencing (Adams et al. 1993), and Serial Analysis of Gene Expression (SAGE, (Velculescu et al. 1995) can decipher complex expression patterns. Much of the resulting data is being deposited on publicly accessible Web sites (Table 1) or is commercially available. Potentially, this information is a valuable resource, but mining the best data and adapting the results for a particular application is challenging. Follow-up and confirmatory studies are time consuming, and this problem will grow with the growth of large-scale expression technologies. A rapid confirmation of differential expression is useful prior to studies of gene function, or before investigating an over-expressed gene as a candidate tumor marker or antigen.
Candidate genes can be identified by mining public databases as in (Lal et al. 1999). Fluorescent-PCR expression comparison (F-PEC) to assess candidate gene expression on a panel of tumor and normal samples. The F-PEC method is based on continuous fluorescent monitoring of PCR products (Wittwer et al. 1997; Morrison et al. 1998) from a cDNA template. F-PEC allows for a quick and low-cost assessment of the expression pattern of a gene, uses commercially available instrumentation, and can be automated. Several candidate tumor markers were identified for glioblastoma multiforme [(GBM) WHO Astrocytoma Grade IV], which is the most common primary brain malignancy in adults, but which can occur at virtually any age (Kleihues et al. 2000). These genetic targets specific for GBM are useful for developing immune-based therapies. Now that expression information is readily available for many cancerous tissues, this approach can be employed to help find markers in other major tumors.
There is a need in the art to diagnose and treat glioblastoma and to identify anticancer drugs.